mt_monashmedfandomcom-20200213-history
L0301P36 - Population Genetics
Levels of Genetics Molecular Level *what the cells say *what gene or mutation creates the trait Transmission Level *what are the traits in the individual *how are the trait disseminated to the next generation Population Level *why are there polymorphisms *why are some traits more advantageous Population Genetics *mathematical model to understand and predict genetic variation at the population level Definitions Population *a group of individuals of the same species *local populations or demes *small groups of population determined by a geographical breakdown Monomorphic *single version of a trait (phenotype) *one allele, one genotype in the entire population - very rare Polymorphism *multiple versions of a trait (phenotype) *multiple alleles, multiple genotypes *can infer an advantage or be neutral **e.g.: single-nucleotide polymorphisms (SNPs): ***most common and smallest variation ***marker of neutral evolution Gene Pool *an abstract ideal: all the genetic information for the population present in the haploid state (no homologous pairs) *in which variation at the genetic level informs the variation at the phenotypic level Phenotype Frequency *proportion of individuals with a particular phenotype *(number with targeted phenotype in a population) ÷ (total number in population) Genotype Frequency *(number with targeted genotype in a population) ÷ (total number in population) *show distribution of genetic variation Allele Frequency *crucial factor in evolution **allele frequencies inform the genotype frequencies for the successive generation *measures the amount of genetic variation in a population *proportion in the gene pool are estimated by counting alleles in a sample of individuals **the population is polymorphic **(number of copies of targeted allele) ÷ (sum of alleles in the population) Calculation Nomenclature *sum of all allele frequencies at a locus = 1 **p = dominant allele **q = recessive allele **p + q = 1 *allele frequencies range from 0 to 1 *if a locus has 2 alleles, there can be 3 genotypes: AA, Aa, aa *in a population of N individuals: **NAA = individuals homozygous (AA) **NAa = individuals heterozygous (Aa) **NaaAA + NAa+ Naa *total no. A alleles in population = 2 NAA + NAa *total no. a alleles in population = 2 Naa + NAa *if p represents the frequency of allele A, and q represents the frequency of allele a: Hardy-Weinberg Law *in a large randomly mating populations: **allele frequencies do not change over time (no migration, mutation or selection) **genotype frequencies can be predicted from allele frequencies *applies for any number of alleles Assumptions *random mating **panmictic population *no selection **genotypes have equal reproductive and survival performance - they contribute equal number of progeny each generation *no mutation **only two alleles are possible *no migration **no gene flow between sub-  populations *infinite population size **no sampling error from generation to generation – no drift Properties In H-W equilibiurm if: *genetic inertia - allele frequencies do not change from one change to another *genotype frequencies are immediately predictable from allele frequencies (and do not change over generations) *freq (AA) = p2 *freq (Aa) = 2pq *freq(aa) = q2 *p2 + 2pq + q2 = 1 *if genotype frequencies are disturbed from these ratios, one generation of random mating will return genotype frequencies to H-W expectations Applications *for predicting genotype frequencies from allele frequencies *the model describes conditions that would result if there were no evolution **patterns of deviation from the model help identify specific mechanisms of evolution *genotype frequencies that deviate from the H-W rule should prompt a search for factors that cause the deviation e.g. heterozygote advantage If the observed genotype frequency varies greatly from the expected (calculated) genotype frequency —> the population is not in H-W equilibrium Carrier Frequency *can be calculated using H-W law *used often in genetic counselling for autosomal recessive disorders when gene has not been identified *disease incidence = q2 *gene frequency = q *carrier incidence = 2pq = 2q(1-q) Risk Calculations *chance(affected) = following multiplied **not affected + chance (carrier) = 0.66 **population carrier incidence **affected egg = 0.5 **affected sperm = 0.5 *if other family member is affected, chance(affected) is much higher than the general population Example: Violations of the H-W Equilibrium New Genetic Variation *mutation **recurrent mutation will change the frequency of an allele in a population **if there is a lot of mutations usually due to an outside source (e.g. toxins) **BUT mutation rates are low and slow Altering Existing Genetic Variation *migration **gene flow: result of the migration of individuals and movements of gametes between populations **new alleles can be added or subtracted from a gene pool = change in allele frequencies *genetic drift **chance event that alters allele frequency **bottleneck effect ***large population goes through a period where N is very small ***population expands however less less genetic variation = lower chance of survival if conditions change *non-random mating **inbreeding leads to homozygosity **outbreeding leads to heterozygosity **assortative mating - choosing particular phenotypes ***e.g. in deaf community, deafness is preferred = spike in deafness rates *selection **deleterious traits = negative selection ***reduced reproductive fitness of those affected ***may be heterozygous or homozygous allele advantage ***e.g. heterozygous advantage ****Sickle-cell disease and malaria Selective Forces *pressures act on phenotypes, not genotypes